private bool TryGetSelectedPeptide(out PeptideGroupDocNode peptideGroup, out PeptideDocNode peptide)
{
peptide = null;
peptideGroup = null;
SequenceTree sequenceTree = _skylineWindow.SequenceTree;
if (null != sequenceTree)
{
PeptideTreeNode peptideTreeNode = sequenceTree.GetNodeOfType<PeptideTreeNode>();
if (null != peptideTreeNode)
{
peptide = peptideTreeNode.DocNode;
}
PeptideGroupTreeNode peptideGroupTreeNode = sequenceTree.GetNodeOfType<PeptideGroupTreeNode>();
if (null != peptideGroupTreeNode)
{
peptideGroup = peptideGroupTreeNode.DocNode;
}
}
return peptide != null;
}
// Support multiple selection (though using peptide settings is more efficient way to do this filtering)
public static List <PeptideGroupTreeNode> PeptideSelection(SequenceTree sequenceTree)
{
var peptideGroupTreeNodes = new List <PeptideGroupTreeNode>();
foreach (var node in sequenceTree.SelectedNodes)
{
PeptideGroupTreeNode peptideGroupTreeNode = null;
var treeNode = node as SrmTreeNode;
if (treeNode != null)
{
peptideGroupTreeNode = treeNode.GetNodeOfType <PeptideGroupTreeNode>();
}
if (peptideGroupTreeNode != null && peptideGroupTreeNode.ChildDocNodes.Cast <PeptideDocNode>().Any(n => n.IsProteomic))
{
peptideGroupTreeNodes.Add(peptideGroupTreeNode);
}
}
return(peptideGroupTreeNodes);
}
// Support multiple selection (though using peptide settings is more efficient way to do this filtering)
public static List <PeptideGroupTreeNode> PeptideSelection(SequenceTree sequenceTree)
{
HashSet <PeptideGroupTreeNode> treeNodeSet = new HashSet <PeptideGroupTreeNode>();
var peptideGroupTreeNodes = new List <PeptideGroupTreeNode>();
foreach (var node in sequenceTree.SelectedNodes)
{
PeptideGroupTreeNode peptideGroupTreeNode = null;
var treeNode = node as SrmTreeNode;
if (treeNode != null)
{
peptideGroupTreeNode = treeNode.GetNodeOfType <PeptideGroupTreeNode>();
}
if (peptideGroupTreeNode == null || !treeNodeSet.Add(peptideGroupTreeNode))
{
continue;
}
if (peptideGroupTreeNode.DocNode.Peptides.Any())
{
peptideGroupTreeNodes.Add(peptideGroupTreeNode);
}
}
return(peptideGroupTreeNodes);
}
public override string GetDisplayText(DisplaySettings settings)
{
return(PeptideGroupTreeNode.ProteinModalDisplayText(this));
}
private void DisplayCalibrationCurve()
{
CalibrationCurveOptions options = Settings.Default.CalibrationCurveOptions;
zedGraphControl.GraphPane.YAxis.Type = zedGraphControl.GraphPane.XAxis.Type
= options.LogPlot ? AxisType.Log : AxisType.Linear;
zedGraphControl.GraphPane.Legend.IsVisible = options.ShowLegend;
_scatterPlots = null;
CalibrationCurve = null;
SrmDocument document = DocumentUiContainer.DocumentUI;
if (!document.Settings.HasResults)
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_No_results_available;
return;
}
PeptideDocNode peptide = null;
PeptideGroupDocNode peptideGroup = null;
SequenceTree sequenceTree = _skylineWindow.SequenceTree;
if (null != sequenceTree)
{
PeptideTreeNode peptideTreeNode = sequenceTree.GetNodeOfType <PeptideTreeNode>();
if (null != peptideTreeNode)
{
peptide = peptideTreeNode.DocNode;
}
PeptideGroupTreeNode peptideGroupTreeNode = sequenceTree.GetNodeOfType <PeptideGroupTreeNode>();
if (null != peptideGroupTreeNode)
{
peptideGroup = peptideGroupTreeNode.DocNode;
}
}
if (null == peptide)
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings
.CalibrationForm_DisplayCalibrationCurve_Select_a_peptide_to_see_its_calibration_curve;
return;
}
PeptideQuantifier peptideQuantifier = PeptideQuantifier.GetPeptideQuantifier(document.Settings, peptideGroup,
peptide);
CalibrationCurveFitter curveFitter = new CalibrationCurveFitter(peptideQuantifier, document.Settings);
if (peptideQuantifier.QuantificationSettings.RegressionFit == RegressionFit.NONE)
{
if (string.IsNullOrEmpty(
peptideQuantifier.QuantificationSettings.NormalizationMethod.IsotopeLabelTypeName))
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_Use_the_Quantification_tab_on_the_Peptide_Settings_dialog_to_control_the_conversion_of_peak_areas_to_concentrations_;
}
else
{
if (!peptide.InternalStandardConcentration.HasValue)
{
zedGraphControl.GraphPane.Title.Text =
string.Format(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_convert_peak_area_ratios_to_concentrations__specify_the_internal_standard_concentration_for__0__, peptide);
}
else
{
zedGraphControl.GraphPane.Title.Text = null;
}
}
}
else
{
if (curveFitter.GetStandardConcentrations().Any())
{
zedGraphControl.GraphPane.Title.Text = null;
}
else
{
zedGraphControl.GraphPane.Title.Text = QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_fit_a_calibration_curve__set_the_Sample_Type_of_some_replicates_to_Standard__and_specify_their_concentration_;
}
}
zedGraphControl.GraphPane.XAxis.Title.Text = curveFitter.GetXAxisTitle();
zedGraphControl.GraphPane.YAxis.Title.Text = curveFitter.GetYAxisTitle();
CalibrationCurve = curveFitter.GetCalibrationCurve();
double minX = double.MaxValue, maxX = double.MinValue;
_scatterPlots = new CurveList();
foreach (var sampleType in SampleType.ListSampleTypes())
{
if (!Options.DisplaySampleType(sampleType))
{
continue;
}
PointPairList pointPairList = new PointPairList();
for (int iReplicate = 0;
iReplicate < document.Settings.MeasuredResults.Chromatograms.Count;
iReplicate++)
{
ChromatogramSet chromatogramSet = document.Settings.MeasuredResults.Chromatograms[iReplicate];
if (!Equals(sampleType, chromatogramSet.SampleType))
{
continue;
}
double?y = curveFitter.GetYValue(iReplicate);
double?x = curveFitter.GetSpecifiedXValue(iReplicate)
?? curveFitter.GetCalculatedXValue(CalibrationCurve, iReplicate);
if (y.HasValue && x.HasValue)
{
PointPair point = new PointPair(x.Value, y.Value)
{
Tag = iReplicate
};
pointPairList.Add(point);
if (!Options.LogPlot || x.Value > 0)
{
minX = Math.Min(minX, x.Value);
}
maxX = Math.Max(maxX, x.Value);
}
}
if (pointPairList.Any())
{
var lineItem = zedGraphControl.GraphPane.AddCurve(sampleType.ToString(), pointPairList,
sampleType.Color, sampleType.SymbolType);
lineItem.Line.IsVisible = false;
lineItem.Symbol.Fill = new Fill(sampleType.Color);
_scatterPlots.Add(lineItem);
}
}
List <string> labelLines = new List <String>();
RegressionFit regressionFit = document.Settings.PeptideSettings.Quantification.RegressionFit;
if (regressionFit != RegressionFit.NONE)
{
if (minX <= maxX)
{
int interpolatedLinePointCount = 100;
if (!options.LogPlot)
{
if (regressionFit == RegressionFit.LINEAR_THROUGH_ZERO)
{
minX = Math.Min(0, minX);
}
if (regressionFit != RegressionFit.QUADRATIC)
{
interpolatedLinePointCount = 2;
}
}
LineItem interpolatedLine = CreateInterpolatedLine(CalibrationCurve, minX, maxX,
interpolatedLinePointCount, Options.LogPlot);
if (null != interpolatedLine)
{
zedGraphControl.GraphPane.CurveList.Add(interpolatedLine);
}
}
labelLines.Add(CalibrationCurve.ToString());
if (CalibrationCurve.RSquared.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_ +
CalibrationCurve.RSquared.Value.ToString("0.####")); // Not L10N
}
if (!Equals(curveFitter.QuantificationSettings.RegressionWeighting, RegressionWeighting.NONE))
{
labelLines.Add(string.Format("{0}: {1}", // Not L10N
QuantificationStrings.Weighting, curveFitter.QuantificationSettings.RegressionWeighting));
}
}
if (options.ShowSelection)
{
double?ySelected = curveFitter.GetYValue(_skylineWindow.SelectedResultsIndex);
double?xSelected = curveFitter.GetCalculatedXValue(CalibrationCurve, _skylineWindow.SelectedResultsIndex);
if (xSelected.HasValue && ySelected.HasValue)
{
ArrowObj arrow = new ArrowObj(xSelected.Value, ySelected.Value, xSelected.Value,
ySelected.Value)
{
Line = { Color = GraphSummary.ColorSelected }
};
zedGraphControl.GraphPane.GraphObjList.Insert(0, arrow);
}
var quantificationResult = curveFitter.GetQuantificationResult(_skylineWindow.SelectedResultsIndex);
if (quantificationResult.CalculatedConcentration.HasValue)
{
labelLines.Add(string.Format("{0} = {1}", // Not L10N
QuantificationStrings.Calculated_Concentration, quantificationResult));
}
else if (!quantificationResult.NormalizedArea.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_The_selected_replicate_has_missing_or_truncated_transitions);
}
}
if (labelLines.Any())
{
TextObj text = new TextObj(TextUtil.LineSeparate(labelLines), .01, 0,
CoordType.ChartFraction, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black),
};
zedGraphControl.GraphPane.GraphObjList.Add(text);
}
}
/// <summary>
/// Create the ordered list of dropdown items, with a rational sort order:
/// First present any sequence matches, sorted by sequence
/// Then present any name, accession, gene, preferredname, or species metadata matches, sorted by the matched metadata field
/// Then present any matches against the description field, sorted by the description text starting at the match location
/// </summary>
public static IList <ListViewItem> CreateListViewItems(IList <ProteinMatch> matches, String searchText, ProteinMatchType matchTypes, int maxCount)
{
var listItems = new SortedList <string, ListViewItem>();
var listUsedMatches = new List <string>();
// First check for matching by sequence
foreach (var match in matches)
{
if (0 != (matchTypes & match.MatchType & ProteinMatchType.sequence))
{
foreach (DigestedPeptide digestedPeptide in match.DigestedPeptides)
{
var listItem = new ListViewItem
{
Text = digestedPeptide.Sequence,
Tag = new StatementCompletionItem
{
Peptide = digestedPeptide.Sequence,
ProteinInfo = match.Protein.ProteinMetadata,
SearchText = searchText
},
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(matchTypes),
null);
listUsedMatches.Add(match.Protein.Name);
listItem.ImageIndex = (int)ImageId.peptide;
var tooltip = new StringBuilder();
tooltip.AppendLine(Resources.StatementCompletionTextBox_CreateListViewItems_Descriptions)
.Append(match.Protein.ProteinMetadata.TextForMatchTypes(matchTypes));
foreach (var name in match.Protein.AlternativeNames)
{
tooltip.AppendLine().Append(name.TextForMatchTypes(matchTypes));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
// Note the leading space in this sort key - we'd like to list sequence matches first
var key = TextUtil.SpaceSeparate(" ", listItem.Text, listItem.ToolTipText); // Not L10N
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
}
}
}
if (listItems.Count >= maxCount)
{
return(new List <ListViewItem>(listItems.Values)); // We used to exit here if we had any matches - but that's frustrating when you're not actually trying to match by sequence
}
// Decide which field not to display on righthand side, based on what's already showing on the left due to View|Targets|By* menu
ProteinMatchType displayMatchType = ProteinMatchType.all;
switch (SequenceTree.ProteinsDisplayMode)
{
case ProteinDisplayMode.ByName:
displayMatchType &= ~ProteinMatchType.name;
break;
case ProteinDisplayMode.ByAccession:
displayMatchType &= ~ProteinMatchType.accession;
break;
case ProteinDisplayMode.ByGene:
displayMatchType &= ~ProteinMatchType.gene;
break;
case ProteinDisplayMode.ByPreferredName:
displayMatchType &= ~ProteinMatchType.preferredName;
break;
}
foreach (var match in matches)
{
// Try matching on name, accession etc - cycle through name, accession, preferredName, gene
for (int bit = 1; bit < (int)ProteinMatchType.all; bit = bit << 1)
{
ProteinMatchType tryType = (ProteinMatchType)bit;
if ((tryType != ProteinMatchType.sequence) && // We already did sequence
(tryType != ProteinMatchType.description) && // And aren't ready for description
(0 != (matchTypes & match.MatchType & tryType) &&
!listUsedMatches.Contains(match.Protein.Name)))
{
var listItem = new ListViewItem();
// Show description, and any other fields we were searching on
if (match.AlternativeName != null)
{
listItem.Text = PeptideGroupTreeNode.ProteinModalDisplayText(match.AlternativeName, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {
ProteinInfo = match.AlternativeName, SearchText = searchText
};
StatementCompletionForm.AddDescription(listItem,
match.AlternativeName.TextForMatchTypes(displayMatchType & ~ProteinMatchType.name), searchText);
}
else
{
listItem.Text = PeptideGroupTreeNode.ProteinModalDisplayText(match.Protein.ProteinMetadata, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {
ProteinInfo = match.Protein.ProteinMetadata, SearchText = searchText
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchType), searchText);
}
listUsedMatches.Add(match.Protein.Name);
listItem.ImageIndex = (int)ImageId.protein;
var tooltip = new StringBuilder();
tooltip.AppendLine(Resources.StatementCompletionTextBox_CreateListViewItems_Descriptions)
.Append(match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchType));
foreach (var altName in match.Protein.AlternativeNames)
{
tooltip.AppendLine().Append(altName.TextForMatchTypes(displayMatchType));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
// We want the sort to be on the particular bit of metadata that we matched
var key = TextUtil.SpaceSeparate(match.Protein.ProteinMetadata.TextForMatchTypes(tryType), listItem.Text, listItem.ToolTipText);
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
break;
}
}
}
if (listItems.Count >= maxCount)
{
return(new List <ListViewItem>(listItems.Values)); // We used to exit here if we had any matches - but that's frustrating when you're not actually trying to match by sequence
}
// Any matches by description?
foreach (var match in matches)
{
if ((0 != (match.MatchType & ProteinMatchType.description)) &&
!listUsedMatches.Contains(match.Protein.Name))
{
ProteinMetadata mainName = match.AlternativeDescription;
string matchName = match.Protein.Name;
var proteinInfo = match.Protein.ProteinMetadata;
if (matchName.Length > MAX_NAME_LENGTH)
{
proteinInfo = proteinInfo.ChangeName(matchName.Substring(0, MAX_NAME_LENGTH) + "..."); // Not L10N
}
var alternativeNames = new List <ProteinMetadata>();
if (mainName == null)
{
mainName = proteinInfo;
}
else
{
alternativeNames.Add(proteinInfo);
}
var listItem = new ListViewItem
{
Text = PeptideGroupTreeNode.ProteinModalDisplayText(mainName, Settings.Default.ShowPeptidesDisplayMode),
ImageIndex = (int)ImageId.protein,
Tag = new StatementCompletionItem {
ProteinInfo = proteinInfo, SearchText = searchText
}
};
StatementCompletionForm.AddDescription(listItem, mainName.TextForMatchTypes(displayMatchType), searchText);
if (match.Protein.AlternativeNames.Count > 0)
{
alternativeNames.AddRange(match.Protein.AlternativeNames);
StringBuilder tooltip = new StringBuilder(Resources.StatementCompletionTextBox_CreateListViewItems_Alternative_Names);
foreach (var altName in alternativeNames)
{
if (altName.Name == mainName.Name)
{
continue;
}
tooltip.AppendLine().Append(altName.TextForMatchTypes(displayMatchType | ProteinMatchType.name));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
}
// We want the sort to be on what we matched in the description, and what follows.
var remains = match.Protein.ProteinMetadata.Description;
int pos = remains.ToLower().IndexOf(searchText.ToLower(), StringComparison.Ordinal);
if (pos > 0)
{
remains = remains.Substring(pos);
}
var key = TextUtil.SpaceSeparate(remains, listItem.Text, listItem.ToolTipText);
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
}
}
return(new List <ListViewItem>(listItems.Values));
}
